HsaINT0072516 @ hg38
Intron Retention
Gene
ENSG00000176884 | GRIN1
Description
glutamate ionotropic receptor NMDA type subunit 1 [Source:HGNC Symbol;Acc:HGNC:4584]
Coordinates
chr9:137163559-137164138:+
Coord C1 exon
chr9:137163559-137163668
Coord A exon
chr9:137163669-137163758
Coord C2 exon
chr9:137163759-137164138
Length
90 bp
Sequences
Splice sites
5' ss Seq
CCGGTGCGT
5' ss Score
9.74
3' ss Seq
CTCTGGGTCCCGGCACACAGGGG
3' ss Score
4.43
Exon sequences
Seq C1 exon
GTCCCACGAGAATGGCTTCATGGAAGACCTGGACAAGACGTGGGTTCGGTATCAGGAATGTGACTCGCGCAGCAACGCCCCTGCGACCCTTACTTTTGAGAACATGGCCG
Seq A exon
GTGCGTTCTCCTTCATCCATTCTCGGGTGGGTTCTCCGTGGGCTGCGGCCTCCCTGGCCAGCAACTGAGGCTCTGGGTCCCGGCACACAG
Seq C2 exon
GGGTCTTCATGCTGGTAGCTGGGGGCATCGTGGCCGGGATCTTCCTGATTTTCATCGAGATTGCCTACAAGCGGCACAAGGATGCTCGCCGGAAGCAGATGCAGCTGGCCTTTGCCGCCGTTAACGTGTGGCGGAAGAACCTGCAGGTAGGGCAGGCCACCCTCCGAGGCCTGGTGCCCAGGGCCCGGCCTGGCCACGGCCCTCCTCCATCCCCGAAGGCCGTGGCACTGGCTCTGGCTCTGGTGGGCAGGACTGGAGCTAGGAGCCATGGCCAGGGGCAGTGGTGAGTGCTCCCAGGGCACGGGGGCAGCACCGGTGGGGGGCTGCCTGCAGGTGGCTGCCCACTGCAAAGCCGGGGCCGAGGGAGGCCACGCACCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000176884:ENST00000460273:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
In the CDS, with uncertain impact
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.007
Domain overlap (PFAM):
C1:
PF0049715=SBP_bac_3=PD(5.0=44.7),PF0006021=Lig_chan=FE(13.9=100)
A:
NA
C2:
PF0006021=Lig_chan=PD(3.4=18.4),PF105624=CaM_bdg_C0=WD(100=59.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCCTGCGACCCTTACTTTTG
R:
GGTTCTTCCGCCACACGTTAA
Band lengths:
174-264
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development